rs7623146

Variant names:

• chr3-63718309-G-A
• rs7623146

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.151 in 152,080 control chromosomes in the GnomAD database, including 1,724 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.15 (1724 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.446

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22994 AN: 151962 Hom.: 1722 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.159

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.151 AC: 23024 AN: 152080 Hom.: 1724 Cov.: 32 AF XY: 0.152 AC XY: 11326 AN XY: 74358

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.157

Alfa AF: 0.147 Hom.: 212

Bravo AF: 0.158

Asia WGS AF: 0.165 AC: 574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.65
DANN	Benign	0.26

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7623146; hg19: chr3-63703985;